Ok so I got my first jeep last Friday 93 4.0 5 speed, 180 on body 80 on motor, pretty much stock.
So it was nice this weekend so I drove it pretty much all day Saturday and all day Sunday. On my way home, the clutch stopped working and I couldnít get it into gear. Somehow it went into second and I drove the rest of the way home like that. (Only like a 1/8 of a mile) Well I knew there was a slight leak coming from the rear seal where the transmission meets the engine. I planned on replacing the seal and the clutch just not this soon. However in my gun-ho approach I just decided to take off the skid plate and see if I could take a look at the transmission leak. Yeah well stupid me didnít know that it was attached and almost dropped the whole transmission. I have it blocked up now and skid plate off, however I broke the 2 middle bolts, they came right out with the rusted female connection almost welded to it. After that happened I started to look at other things and determined that my clutch master cylinder doesnít seem to be working when I pump the clutch the fluid doesnít go anywhere.
So my first question is how do I replace the 2 bolts?
Question 2 is now that I have it all off should I just replace everything now? meaning clutch kit master cyl. stuff like that?
Question 3 I plan to repaint and heculin or rhino the under body and frame to stop some rust and if I drop the transmission it would be the perfect time to do it while its out of the way. Any help with this would also be appreciated too.

Its up to u if u want to replace everything. Cause if u do have to do the same job over. Personally I would while u have it apart but money might be a issue. But if u do wait at least u had it apart so it should come aprt easyer. For the bolt maybe a "easyout" or drill it out carefully!